[2024-01-24 14:07:14,852] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:14,854] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:14,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b513725-f540-45f9-8c2c-7a7899a4cf8c/dqc_reference
[2024-01-24 14:07:16,149] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:16,150] [INFO] Task started: Prodigal
[2024-01-24 14:07:16,151] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d790ba6-a167-48f6-bab0-5cb47f85a368/GCF_000169175.1_ASM16917v1_genomic.fna.gz | prodigal -d GCF_000169175.1_ASM16917v1_genomic.fna/cds.fna -a GCF_000169175.1_ASM16917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:08:02,399] [INFO] Task succeeded: Prodigal
[2024-01-24 14:08:02,400] [INFO] Task started: HMMsearch
[2024-01-24 14:08:02,400] [INFO] Running command: hmmsearch --tblout GCF_000169175.1_ASM16917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b513725-f540-45f9-8c2c-7a7899a4cf8c/dqc_reference/reference_markers.hmm GCF_000169175.1_ASM16917v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:08:02,803] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:08:02,805] [INFO] Found 6/6 markers.
[2024-01-24 14:08:02,880] [INFO] Query marker FASTA was written to GCF_000169175.1_ASM16917v1_genomic.fna/markers.fasta
[2024-01-24 14:08:02,880] [INFO] Task started: Blastn
[2024-01-24 14:08:02,880] [INFO] Running command: blastn -query GCF_000169175.1_ASM16917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b513725-f540-45f9-8c2c-7a7899a4cf8c/dqc_reference/reference_markers.fasta -out GCF_000169175.1_ASM16917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:03,470] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:03,475] [INFO] Selected 33 target genomes.
[2024-01-24 14:08:03,475] [INFO] Target genome list was writen to GCF_000169175.1_ASM16917v1_genomic.fna/target_genomes.txt
[2024-01-24 14:08:03,515] [INFO] Task started: fastANI
[2024-01-24 14:08:03,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d790ba6-a167-48f6-bab0-5cb47f85a368/GCF_000169175.1_ASM16917v1_genomic.fna.gz --refList GCF_000169175.1_ASM16917v1_genomic.fna/target_genomes.txt --output GCF_000169175.1_ASM16917v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:08:37,955] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:37,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b513725-f540-45f9-8c2c-7a7899a4cf8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:08:37,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b513725-f540-45f9-8c2c-7a7899a4cf8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:08:37,959] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:08:37,959] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:08:37,960] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Microscilla marina	strain=ATCC 23134	GCA_000169175.1	1027	1027	type	True	100.0	3181	3190	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:08:37,961] [INFO] DFAST Taxonomy check result was written to GCF_000169175.1_ASM16917v1_genomic.fna/tc_result.tsv
[2024-01-24 14:08:37,961] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:08:37,962] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:08:37,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b513725-f540-45f9-8c2c-7a7899a4cf8c/dqc_reference/checkm_data
[2024-01-24 14:08:37,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:08:38,055] [INFO] Task started: CheckM
[2024-01-24 14:08:38,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000169175.1_ASM16917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000169175.1_ASM16917v1_genomic.fna/checkm_input GCF_000169175.1_ASM16917v1_genomic.fna/checkm_result
[2024-01-24 14:10:39,416] [INFO] Task succeeded: CheckM
[2024-01-24 14:10:39,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:10:39,441] [INFO] ===== Completeness check finished =====
[2024-01-24 14:10:39,442] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:10:39,442] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000169175.1_ASM16917v1_genomic.fna/markers.fasta)
[2024-01-24 14:10:39,443] [INFO] Task started: Blastn
[2024-01-24 14:10:39,443] [INFO] Running command: blastn -query GCF_000169175.1_ASM16917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b513725-f540-45f9-8c2c-7a7899a4cf8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000169175.1_ASM16917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:40,247] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:40,251] [INFO] Selected 32 target genomes.
[2024-01-24 14:10:40,251] [INFO] Target genome list was writen to GCF_000169175.1_ASM16917v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:10:40,304] [INFO] Task started: fastANI
[2024-01-24 14:10:40,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d790ba6-a167-48f6-bab0-5cb47f85a368/GCF_000169175.1_ASM16917v1_genomic.fna.gz --refList GCF_000169175.1_ASM16917v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000169175.1_ASM16917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:11:17,288] [INFO] Task succeeded: fastANI
[2024-01-24 14:11:17,296] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:11:17,296] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000169175.1	s__Microscilla marina	100.0	3181	3190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Microscillaceae;g__Microscilla	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001890965.1	s__Microscilla sp001890965	77.2223	663	3190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Microscillaceae;g__Microscilla	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003483885.1	s__Microscilla sp003483885	76.7289	541	3190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Microscillaceae;g__Microscilla	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:11:17,298] [INFO] GTDB search result was written to GCF_000169175.1_ASM16917v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:11:17,299] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:11:17,301] [INFO] DFAST_QC result json was written to GCF_000169175.1_ASM16917v1_genomic.fna/dqc_result.json
[2024-01-24 14:11:17,301] [INFO] DFAST_QC completed!
[2024-01-24 14:11:17,301] [INFO] Total running time: 0h4m2s